Re: [modeller_usage] setting the DEVIATION

[Karsten Suhre <>]

Hi Ori,

> Does anyone know how to control the XYZ randomization parameter DEVIATION?
> I tried modifying its value using a simple SET DEVIATION = 0.0, but nothing
> happens. The reasults are the same as for the default value of 4.0.

Try to generate more than one models in one go by using the following 
commands:

SET STARTING_MODEL= 1               # index of the first model
SET ENDING_MODEL  = 10               # index of the last model

Also, I understand that the initial random seed has to be a negative value in 
order to produce different models in different runs, e.g. use

SET RAND_SEED     = -42

I hope this helps,

Kind regards, Karsten.

PS: Don't set DEVIATION to zero if you want different models.

PPS: You can also try different MD_LEVEL parameters to get different models 
(of course the models will be of different quality, but in some applications, 
i.e. for molecular replacement, this may be a good idea)

SET MD_LEVEL = 'refine_3'